BIOMAT Database Logo BIOMAT Database Logo

Slide into action: dynamic shuttling of HIV reverse transcriptase on nucleic acid substrates. 2008

Shixin Liu, and Elio A Abbondanzieri, and Jason W Rausch, and Stuart F J Le Grice, and Xiaowei Zhuang
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.

The reverse transcriptase (RT) of human immunodeficiency virus (HIV) catalyzes a series of reactions to convert single-stranded viral RNA into double-stranded DNA for host cell integration. This process requires a variety of enzymatic activities, including DNA polymerization, RNA cleavage, strand transfer, and strand displacement synthesis. We used single-molecule fluorescence resonance energy transfer to probe the interactions between RT and nucleic acid substrates in real time. RT was observed to slide on nucleic acid duplexes, rapidly shuttling between opposite termini of the duplex. Upon reaching the DNA 3' terminus, RT can spontaneously flip into a polymerization orientation. Sliding kinetics were regulated by cognate nucleotides and anti-HIV drugs, which stabilized and destabilized the polymerization mode, respectively. These long-range translocation activities facilitate multiple stages of the reverse transcription pathway, including normal DNA polymerization and strand displacement synthesis.

UI MeSH Term Description Entries
D007700 Kinetics The rate dynamics in chemical or physical systems.
D008958 Models, Molecular Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures. Molecular Models,Model, Molecular,Molecular Model
D009693 Nucleic Acid Hybridization Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503) Genomic Hybridization,Acid Hybridization, Nucleic,Acid Hybridizations, Nucleic,Genomic Hybridizations,Hybridization, Genomic,Hybridization, Nucleic Acid,Hybridizations, Genomic,Hybridizations, Nucleic Acid,Nucleic Acid Hybridizations
D009711 Nucleotides The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed) Nucleotide
D011485 Protein Binding The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments. Plasma Protein Binding Capacity,Binding, Protein
D011487 Protein Conformation The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain). Conformation, Protein,Conformations, Protein,Protein Conformations
D002232 Carbocyanines Compounds that contain three methine groups. They are frequently used as cationic dyes used for differential staining of biological materials. Carbocyanine
D004279 DNA, Viral Deoxyribonucleic acid that makes up the genetic material of viruses. Viral DNA
D005456 Fluorescent Dyes Chemicals that emit light after excitation by light. The wave length of the emitted light is usually longer than that of the incident light. Fluorochromes are substances that cause fluorescence in other substances, i.e., dyes used to mark or label other compounds with fluorescent tags. Flourescent Agent,Fluorescent Dye,Fluorescent Probe,Fluorescent Probes,Fluorochrome,Fluorochromes,Fluorogenic Substrates,Fluorescence Agents,Fluorescent Agents,Fluorogenic Substrate,Agents, Fluorescence,Agents, Fluorescent,Dyes, Fluorescent,Probes, Fluorescent,Substrates, Fluorogenic
D001665 Binding Sites The parts of a macromolecule that directly participate in its specific combination with another molecule. Combining Site,Binding Site,Combining Sites,Site, Binding,Site, Combining,Sites, Binding,Sites, Combining

Related Publications

Shixin Liu, and Elio A Abbondanzieri, and Jason W Rausch, and Stuart F J Le Grice, and Xiaowei Zhuang
HIV-1 nucleocapsid traps reverse transcriptase on nucleic acid substrates.
November 2008, Biochemistry,
Shixin Liu, and Elio A Abbondanzieri, and Jason W Rausch, and Stuart F J Le Grice, and Xiaowei Zhuang
Two step binding of HIV-1 reverse transcriptase to nucleic acid substrates.
August 1993, Nucleic acids research,
Shixin Liu, and Elio A Abbondanzieri, and Jason W Rausch, and Stuart F J Le Grice, and Xiaowei Zhuang
Amino acid phosphoramidate nucleotides as alternative substrates for HIV-1 reverse transcriptase.
January 2007, Angewandte Chemie (International ed. in English),
Shixin Liu, and Elio A Abbondanzieri, and Jason W Rausch, and Stuart F J Le Grice, and Xiaowei Zhuang
Mapping of nucleic acid binding in proteolytic domains of HIV-1 reverse transcriptase.
July 1993, Biochemistry,
Shixin Liu, and Elio A Abbondanzieri, and Jason W Rausch, and Stuart F J Le Grice, and Xiaowei Zhuang
The 'helix clamp' in HIV-1 reverse transcriptase: a new nucleic acid binding motif common in nucleic acid polymerases.
November 1994, Nucleic acids research,
Shixin Liu, and Elio A Abbondanzieri, and Jason W Rausch, and Stuart F J Le Grice, and Xiaowei Zhuang
Dynamic binding orientations direct activity of HIV reverse transcriptase.
May 2008, Nature,
Shixin Liu, and Elio A Abbondanzieri, and Jason W Rausch, and Stuart F J Le Grice, and Xiaowei Zhuang
Pre-existing distortions in nucleic acid structure aid polypurine tract selection by HIV-1 reverse transcriptase.
May 2002, The Journal of biological chemistry,
Shixin Liu, and Elio A Abbondanzieri, and Jason W Rausch, and Stuart F J Le Grice, and Xiaowei Zhuang
Broad-spectrum aptamer inhibitors of HIV reverse transcriptase closely mimic natural substrates.
October 2011, Nucleic acids research,
Shixin Liu, and Elio A Abbondanzieri, and Jason W Rausch, and Stuart F J Le Grice, and Xiaowei Zhuang
The orientation of binding of human immunodeficiency virus reverse transcriptase on nucleic acid hybrids.
October 1995, Nucleic acids research,
Shixin Liu, and Elio A Abbondanzieri, and Jason W Rausch, and Stuart F J Le Grice, and Xiaowei Zhuang
Phosphodiester substrates for incorporation of nucleotides in DNA using HIV-1 reverse transcriptase.
September 2009, Chembiochem : a European journal of chemical biology,
Copied contents to your clipboard!